3. Simulations

An MDMC simulation requires a Universe, and one or more Atom objects, which can be combined into one or more Molecule objects. These atoms and molecules must be added to a Universe.

Atoms can have bonded (Bond, BondAngle, Dihedral) interactions or non-bonded (Dispersive, Coulombic) interactions applied to them. For a simulation to run, a functional form must be specified for each interaction: for instance a Dispersive interaction could have a LennardJones or a Buckingham interaction function applied to it.

Once the Universe is setup, it should be passed to a Simulation object. This controls the properties of the simulation, such as which engine will be used and what the thermodynamic conditions are. It is then possible to minimize() and run() the Simulation. The results of the simulation can then be accessed through Simulation, for example via the property trajectory.

For in-depth examples of these please see the related tutorials, particularly Building a Universe and Running a Simulation.

As mentioned in the Introduction, MDMC can be used purely to aid the setup of MD simulations, without performing a refinement. It is possible to:

fill() and solvate() a Universe

read() in configuration and topology (except Dispersive interactions) from CIF files (see Reading atoms from configuration files tutorial)

view() the configuration and topology in a GUI, to check the setup is correct

Use add_force_field() to apply established force fields (e.g. OPLSAA) to the topology to set the interaction functions and parameters (see Applying a FieldField)